diff --git a/pkgs/sqlite.yaml b/pkgs/sqlite.yaml
deleted file mode 100644
index a5f8ac2a1..000000000
--- a/pkgs/sqlite.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-extends: [autotools_package]
-dependencies:
-  build: [readline]
-
-sources:
-  - url: https://sqlite.org/2013/sqlite-autoconf-3071700.tar.gz
-    key: tar.gz:r72g2c5ktzsmbakvituct2mf6elbyclk
diff --git a/pkgs/sqlite/cygwin_config_guess.patch b/pkgs/sqlite/cygwin_config_guess.patch
new file mode 100644
index 000000000..e5f2113ad
--- /dev/null
+++ b/pkgs/sqlite/cygwin_config_guess.patch
@@ -0,0 +1,12 @@
+--- a/config.guess	2016-11-30 15:12:41.668793100 +0100
++++ b/config.guess	2016-11-30 15:13:49.883718600 +0100
+@@ -797,6 +797,9 @@
+     amd64:CYGWIN*:*:*)
+ 	echo x86_64-unknown-cygwin
+ 	exit ;;
++    x86_64:CYGWIN*:*:*)
++	echo x86_64-unknown-cygwin
++	exit ;;
+     p*:CYGWIN*:*)
+ 	echo powerpcle-unknown-cygwin
+ 	exit ;;
diff --git a/pkgs/sqlite/sqlite.yaml b/pkgs/sqlite/sqlite.yaml
new file mode 100644
index 000000000..add7b7081
--- /dev/null
+++ b/pkgs/sqlite/sqlite.yaml
@@ -0,0 +1,16 @@
+extends: [autotools_package]
+dependencies:
+  build: [readline]
+
+build_stages:
+  - when: platform == 'Cygwin'
+    name: patch
+    before: configure
+    files: [cygwin_config_guess.patch]
+    handler: bash
+    bash: |
+      patch -up1 < _hashdist/cygwin_config_guess.patch
+
+sources:
+  - url: https://sqlite.org/2013/sqlite-autoconf-3071700.tar.gz
+    key: tar.gz:r72g2c5ktzsmbakvituct2mf6elbyclk